A Synergistic DNA Walker-Track System with Tailored Spatial Compatibility for Rapid and Ultrasensitive...

Despite their considerable promise in biosensing applications, current DNA walkers remain constrained by insufficient spatial compatibility between the walker and the track. This limitation restricts the walking speed and operational continuity, which in turn hampers detection sensitivity and overall efficiency. Herein, we engineered a synergistic pairing system comprising a novel DNA-confined matrix track (DCM-track) assembled from DNA cube monomers and a target-triggered tetrahedral DNA walker (TDC-walker), which together enable rapid and ultrasensitive electrochemical biosensing of target MUC1. Unlike traditional DNA walker-track systems with insufficient spatial compatibility, where disordered and irregularly spaced tracks cause operational failures of DNA walkers such as derailment and interrupted movement, the DCM-track features a structural design with tailored spatial compatibility, in which the geometry and linkage distance of its assembly monomers are precisely tailored to match the moving trajectory and step size of the TDC-walker. This high spatial compatibility maximizes dynamic perception and programmed response between the walker and its designated track, which in turn improves walking efficiency and operational lifespan of the TDC-walker, thereby leading to a marked improvement in the overall efficiency and sensitivity of the detection platform. Furthermore, biochemical experiments and kinetic investigations validated that this synergistic system reached equilibrium within 10 min and achieved a final walking efficiency of 81.69%. This performance represented a 6-fold increase in speed and a 2.8-fold enhancement in efficiency compared with conventional walker systems. As a proof of concept, the fabricated electrochemical biosensor achieved rapid and ultrasensitive detection of MUC1 with a 63.94 ag/mL detection limit, holding great promise for early clinical applications.